scPDB - 2vn1 entry

Protein Data Bank Entry:

PDB ID : 2vn1

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2008-01-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peptidylprolyl isomerase
ID:	Q8I4V8_PLAF7
AC:	Q8I4V8
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	36329
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	60 %
B	40 %

Ligand binding site composition:

B-Factor:	27.993
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.091	1471.500

% Hydrophobic	% Polar
45.87	54.13
According to VolSite

Ligand :

HET Code:	FK5
Formula:	C44H69NO12
Molecular weight:	804.018 g/mol
DrugBank ID:	DB00864
Buried Surface Area:	65.85 %
Polar Surface area:	178.36 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	3
Rings:	4
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
0.0537895	32.8638	15.1557

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C37	CD1	LEU- 23	3.89	0	Hydrophobic	false
C5	CZ	TYR- 44	4	0	Hydrophobic	false
C34	CG2	VAL- 45	4.26	0	Hydrophobic	false
C23	CG2	VAL- 45	4.1	0	Hydrophobic	false
C35	CE1	PHE- 55	4.24	0	Hydrophobic	false
O6	OD2	ASP- 56	2.69	157.76	H-Bond (Ligand Donor)	false
C33	CB	SER- 57	3.59	0	Hydrophobic	false
C29	CB	PHE- 59	4.15	0	Hydrophobic	false
C31	CB	PHE- 59	4.11	0	Hydrophobic	false
C33	CB	PHE- 59	4.21	0	Hydrophobic	false
C42	CD1	PHE- 59	3.7	0	Hydrophobic	false
C43	CZ	PHE- 59	3.84	0	Hydrophobic	false
C17	CE1	PHE- 65	4.02	0	Hydrophobic	false
C36	CD1	PHE- 65	3.76	0	Hydrophobic	false
C41	CE1	PHE- 65	3.64	0	Hydrophobic	false
C4	CE2	PHE- 65	3.48	0	Hydrophobic	false
O10	O	GLU- 73	2.62	131.15	H-Bond (Ligand Donor)	false
C3	CB	VAL- 74	4.4	0	Hydrophobic	false
C4	CG1	VAL- 74	4.14	0	Hydrophobic	false
C3	CG1	ILE- 75	4.13	0	Hydrophobic	false
C30	CG2	ILE- 75	4.06	0	Hydrophobic	false
O2	N	ILE- 75	3.14	150.56	H-Bond (Protein Donor)	false
C5	CZ2	TRP- 78	3.86	0	Hydrophobic	false
C3	CE2	TRP- 78	3.43	0	Hydrophobic	false
C18	CD	LYS- 90	3.97	0	Hydrophobic	false
C38	CD	LYS- 90	4.2	0	Hydrophobic	false
C30	CE1	TYR- 101	4.03	0	Hydrophobic	false
C35	CZ	TYR- 101	4.28	0	Hydrophobic	false
C42	CE1	TYR- 101	4	0	Hydrophobic	false
O3	OH	TYR- 101	2.75	174.62	H-Bond (Protein Donor)	false
C12	SG	CYS- 106	4.44	0	Hydrophobic	false
C35	SG	CYS- 106	3.94	0	Hydrophobic	false
C35	CD1	ILE- 110	3.61	0	Hydrophobic	false
C38	CB	GLU- 121	4.08	0	Hydrophobic	false
O10	O	HOH- 2062	2.69	179.99	H-Bond (Protein Donor)	false